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Evgeniia Chikina
I am Bioinformatic Master student who previously graduated from Medical University. I use all of my medical and biological knowledge to combine with the world of computer science. At the moment I have especially good knowledge and skills in analyzing RNA sequencing data. Now and in the future I try to develop and gain knowledge in various aspects of bioinformatics, in particular in such areas as: RNA-seq, epigenetics, multi-omics data analysis.
Education
Master degree, Applied Mathematics and Informatics, Bioinformatics and System Biology
ITMO University
Saint-Petersburg, Russia
Current - 2020
- Thesis: Metabolic Modules Identification in Single-Cell Data
- Course Project: Identifying Metabolic Modules in TCGA Datasets
- Semester Project: Effects of Background RNA Noise on Differential Expression Results in scRNA-seq
Specialist degree (with honors), Pediatrician
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2020 - 2014
- Pediatrician
Basic Education
School №197 with advanced study of natural sciences (physics, chemistry, biology)
N/A
Saint-Petersburg, Russia
2014 - 2012
- 10-11th grade
- Advanced biology, chemistry, start of medical training
Gymnasuim №107
N/A
Saint-Petersburg, Russia
2012 - 2008
- 6-9th grade
School №118
N/A
Saint-Petersburg, Russia
2008 - 2003
- 1-5th grade
Research Projects
Metabolic Modules Identification in Single-Cell Data
ITMO University
Saint-Petersburg, Russia
Current - 2021
- Thesis
- Main goal of the project is to extend applications of the GAM-clustering tool on the single-cell RNA-seq data. In order to find optimal clustering algorithm performed and analysed multiple clustering strategies for the single-cell RNA-seq data. Used trajectories and gene set enrichment analysis for biological interpretation of the results. Involved in the modification of the tool.
Identifying Metabolic Modules in TCGA Datasets
ITMO University
Saint-Petersburg, Russia
2021
- Course Project
- With previousy developed GAM-clustering algorithm analyzed TCGA datasets (LUSC) - bulk RNA-seq data. Identified metabolic modules and performed biological analysis of them. During work was involved in the modification of the tool and testing.
Effects of Background RNA Noise on Differential Expression Results in scRNA-seq
ITMO University
Saint-Petersburg, Russia
2020
- Performed standart analysis of the single-cell data with Seurat pipeline and integration of multiple samples using SCTransform intgration. With help of
DropletUtilsR package identified ambient RNA and tried to estimate the impact of it on the differential expression results.
Other Projects
DiveR ShinyApp
Perdana University (Students Project)
N/A
2022
- DiveR is a graphical user interface (GUI)-based web application hosted on R Shiny for the visualization of DiMA results, a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses.
- Modifications of ShinyApp scripts
- https://github.com/pendy05/DiveR
Conferences
Nationwide scientific forum of students and young scientists with international participation «Student science – 2018»
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2018
- Research Work: “Study of microbiological landscape and microorganism susceptibility analysis to antibacterial drugs in the neonatal and premature infants intensive care department, cardiac intensive care department and neonatal pathology department for the period from 2014 to 2017”
- Pharmacology Section: 3d degree diploma
Publications
Gainullina A., Chikina E., Mogilenko D. et al. Open Source ImmGen: network perspective on metabolic diversity among mononuclear phagocytes, bioRxiv 2020.07.15.204388; doi: https://doi.org/10.1101/2020.07.15.204388 (under review)
N/A
N/A
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Achievements
NGSprint Hackaton
Discord, online
2021
Annual University Pediatrics Olympiad
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2018
- 1st degree diploma
Olympiad in Propaedeutics of Children’s Diseases at St. Petersburg State Pediatric Medical University
Saint-Petersburg State Pediatric Medical University
Saint-Petersburg, Russia
2017
- 2nd degree diploma
Teaching experience
Chemistry/Biology School Tutor
N/A
Saint-Petersburg, Russia
2020 - 2018
- I was teaching 6-9th grade school students chemistry and biology to increase their knowledge in the field and in some cases helped studying for school exams.
Courses
Introduction to Probability and Data with R (en)
Duke University
Coursera, Online
2022
Molecular biology of the cell (ru)
Bioinformatics Institute
Stepik, Online
2020
Programming in Python (ru)
Bioinformatics Institute
Stepik, Online
2019